ExPASy: SIB bioinformatics resource portal
By Panu Artimo, Manohar Jonnalagedda, Konstantin Arnold, Delphine Baratin, Gábor Csárdi, Edouard De Castro, S. Duvaud, Volker Flegel, Arnaud Fortier, Elisabeth Gasteiger and 11 more. Nucleic Acids Res., 2012
2,059 citations recorded by the source corpus.
ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a ‘decentralized’ way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across ‘selected’ resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/bfada4dd6e30ed53835b0ab326f16140922ebf31
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In Molecular Biology
- Torsten Schwede
- Lorenza Bordoli
- Gabriel Studer
- Antoine Daina
- Adrian M. Altenhoff
- J. Haas
- Konstantin Arnold
- Vincent Zoete
Citations in the corpus
- Use of DNA metabarcoding for stomach content analysis in the invasive lionfish Pterois volitans in Puerto Rico (2016, methodology): “All cleaned reads were translated into amino acids using ExPASy Translate tool (Artimo et al. 2012) and MEGA 6 (Tamura et al. 2013) to further support accurate matches to references in both databases.”
- PDBe: improved accessibility of macromolecular structure data from PDB and EMDB (2015, background): “For enzymes, information is shown on the reaction catalysed and other relevant comments on function or biological availability of the particular enzyme obtained from enzyme resources such as IntEnz (45), Brenda (46) and Expasy (47).”
- BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA (2012, methodology): “In this respect it is different from other enzyme databases which are specialized either on the nomenclature [ExplorEnz, ENZYME (20), IntEnz (21)], on the metabolic pathways (e.g. KEGG, MetaCyc) or on specific classes of enzymes [e.g. Merops (22), MODOMICS (23), CAZy (24), Kinomer (25)].”
- The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases (2015, background): “All SIB groups are regularly invited to list their resources on ExPASy, SIB’s bioinformatics resource portal www.expasy.org (7).”